CARMEL-BY-THE-SEA, Calif. — A group of teenagers huddled at the foot of a statue of Junípero Serra at the Carmel Mission on Monday, there to pay homage to the Spaniard who helped colonize California in the 18th century. Only a day earlier, vandals had toppled the six-foot figure and doused it with paint, writing “saint of genocide” on a nearby triangle of stone. But now the statue was upright and scrubbed clean for visitors.

Catholic Church officials said the vandalism was the first of its kind at the mission, timed to Pope Francis’ visit to the United States, during which he elevated Father Serra to sainthood at a Mass at the Basilica of the National Shrine of the Immaculate Conception in Washington. The attack also came just hours before parishioners planned to honor Father Serra, a revered former Carmel resident whose celebrity attracts thousands of tourists each year to this quiet hamlet along Monterey Bay.

The police continue to investigate what they have called a hate crime. And the episode threatens to inflame a decades-old wound between the Roman Catholic Church and Native Americans who contend that Father Serra was more oppressor than saint. Historians agree that he forced Native Americans to abandon their tribal culture and convert to Christianity, and that he had them whipped and imprisoned and sometimes worked or tortured to death.

In the vandalism case, there are so far no suspects, and no group has claimed responsibility, said an investigator on the case, Sgt. Luke Powell of the city’s police force.

A security camera that might have identified the intruders was not working when the vandalism occurred, Sergeant Powell said. A private guard hired to patrol the grounds told the police that he had not seen or heard a disturbance. And to complicate matters, Sergeant Powell said, parishioners and others walked through the crime scene, making even the paint cans left by the vandals useless as evidence.

Visitors and mission representatives sought healing this week, while Native American tribal members who opposed Father Serra’s sainthood sought to distance themselves from the desecration, fearing a backlash. Pope Francis, after all, had praised the missionary as “one of the founding fathers of the United States,” someone who sacrificed a great deal to spread the gospel of Christianity in America. And as America’s first Latino saint, Father Serra holds particular appeal in this state, where Latinos are the dominant ethnic group.

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A church official praised “a sacred space to both Christian people and Native Americans.”CreditJim Wilson/The New York Times

Not everyone is a fan.

“I am against Serra being made a saint,” said Louise J. Miranda Ramirez, tribal chairwoman of the Ohlone Costanoan Esselen Nation, which represents Native American tribal members from the coast of Central and Northern California. “But just because we objected to the canonization, that doesn’t mean we did it.”

The Rev. Bob Brady, a Franciscan priest who lives in Oakland and attended Mass at the mission on Monday, said one of the priests there had described the vandalism “as a punch in the gut.” He added of the vandals, “This came from someone’s pain, and they need to know of our forgiveness.”

Father Serra was born in 1713 on the island of Majorca and came to this area in 1768, wielding his influence not only to convert Native Americans to Christianity, but also to bolster Spain’s economic and political interests. In 1770, he founded Carmel Mission, the second of California’s 21 missions, which served as centers of cattle and grain production in addition to being hubs for the expansion of Catholicism. Father Serra’s motto, which is printed on water bottles and other souvenirs sold in the gift shop, was, “Always go forward and never turn back.”

Most Californians agree that colonization came at a price. Thousands of Native Americans died after being exposed to European diseases. Those who survived were forced to give up tribal customs and submit to the demands of their Christian overlords — from observing rites like baptism to enduring physical abuse and working conditions that resembled slavery.

For many Native Americans, Ms. Miranda Ramirez said, the colonization of California was tantamount to genocide. Villagers were rounded up, shackled or flogged if they failed to follow the missionaries’ Catholic code. Steven W. Hackel, a history professor at the University of California, Riverside, and the author of “Junípero Serra: California’s Founding Father,” wrote in his book that the newly canonized saint was both a visionary and an imperialist whose attitudes reflected the era in which he lived.

The spread of Christianity in California was as much a governing force as spiritual practice. According to the website of the California Missions Resource Center, Spanish conquerors had promising results backing missionaries who settled areas in the American Southwest and the Río de la Plata region of Latin America. Missionaries taught school and farming and imposed what they believed to be societal order.

During a trip to Bolivia in July, Pope Francis, who was born in Argentina, spoke of the subjugation of local cultures by Catholics, saying, “I humbly ask forgiveness, not only for the offense of the church herself, but also for crimes committed against the native peoples during the so-called conquest of America.” But that has done little to sway the attitudes of Native Americans here.

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The Carmel Mission, established in 1770, was the second of California’s 21 missions.CreditJim Wilson/The New York Times

Last Wednesday, several hundred people gathered at 1 p.m. in the mission courtyard to watch the canonization Mass on a live broadcast from Washington. As the pope named Father Serra a saint, bells clanged from a tower. Twenty feet away, about two dozen Native Americans had gathered in a cemetery containing the remains of forebears who had worked at the mission, their graves adorned by rows of stones, wooden crosses and plate-size abalone shells.

Jewel Gentry, the California missions coordinator for the Diocese of Monterey, said the tribal gatherers were welcome. “It’s a sacred space to both Christian people and Native Americans,” he said.

But in the early hours of Saturday, not long before the parishioners planned to celebrate Father Serra’s canonization with a Mass and barbecue, vandals climbed over one of the low stone walls that flank the mission, Sergeant Powell said. There, they found an unlocked utility closet containing buckets of dark green and eggshell-colored paint. After toppling and painting the statue, the vandals wandered over to a sign with Father Serra’s name on it and wrote: “This man is responsible for genocide. Greed is evil.” (The sign has been removed, Sergeant Powell said.) Paint was also splattered on the basilica’s front doors and on two Christian headstones in the graveyard.

The vandalism was discovered when a priest went to open the basilica about 7 a.m. for an early Mass. According to a spokeswoman for the mission, priests at the morning Masses asked parishioners to help clean the courtyard and posted a note on Facebook seeking other volunteers. Townspeople brought sponges, buckets, cleanser and a pressure washer to remove as much of the paint as possible before 11 a.m., when the Mass to celebrate the canonization was scheduled to start. The evidence was mostly gone by Monday, except for random spatters and a patch of dry paint on the ground below the statue.

“It was devastating,” said Rudy Rosales, a former tribal chairman of the Ohlone Costanoan Esselen Nation, who is Catholic and tends the Native American graves in the mission cemetery. “I can’t think of someone doing this. Three-quarters of our tribe is Catholic.” He said he neither supported nor opposed the canonization of Father Serra, although it has angered some in his tribe. “I’ve had Indians call me a Mission-token Indian,” he said, adding, “Everyone has been through so much.”

On Monday, the paint splatters in the dirt were a momentary curiosity for the teenage pilgrims, students from Thomas More School in San Jose. They formed two lines and walked into the basilica singing “Salve Regina,” their lilting voices reverberating against the walls. Boys and girls, some wearing lace veils and carrying rosary beads, whispered Hail Marys, while a priest blessed them with a relic, a splinter of the coffin Father Serra was buried in.

The Rev. Gerard Hogan, the school chaplain, said of the vandalism, “We were sad to see that.” He wondered, “If you sense an injustice, why would you seek an injustice as payback?”

A version of this article appears in print on , on Page A1 of the New York edition with the headline: Sainthood of Serra Reopens Wounds of Colonialism in California . Order Reprints | Today’s Paper | Subscribe